TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository

• Published in: Journal of translational medicine Vol. 19; no. 1; pp. 1 - 15
• Main Authors: Zhao, Yingdong, Li, Ming-Chung, Konaté, Mariam M., Chen, Li, Das, Biswajit, Karlovich, Chris, Williams, P. Mickey, Evrard, Yvonne A., Doroshow, James H., McShane, Lisa M.
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 22.06.2021; BioMed Central; BMC
• Subjects: Analysis; Cancer; Cell culture; Count; Data analysis; DNA microarrays; FPKM; Gene expression; Genetic aspects; Genetic research; Medical research; Normalization; Quantification measures; Reading frames; Ribonucleic acid; RNA; RNA sequencing; TPM; Transcription; Tumors; Xenografts; United States

Background In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Severa...